Switch GitLab to stock Amazon Linux 2 AMI (#4188)

[hannes-ucsc]

Connected issue: #4188

Checklist

Author

• Target branch is develop
• Name of source branch matches issues/<GitHub handle of author>/<issue#>-<slug>
• PR title references the connected issue
• PR title matches¹ title of connected issue _{or comment in PR explains why they're different}
• Title of at least one commit references connected issue
• PR is connected to issue via Zenhub
• PR description links to connected issue
• Added partial label to PR _{or this PR completely resolves the connected issue}

¹ when the issue title describes a problem, the PR title is Fix: followed by the issue title

Author (reindex)

• Added r tag to commit title _{or this PR does not require reindexing}
• Added reindex label to PR _{or this PR does not require reindexing}

Author (chains)

• This PR is blocked by previous PR in the chain _{or this PR is not chained to another PR}
• Added base label to the blocking PR _{or this PR is not chained to another PR}
• Added chained label to this PR _{or this PR is not chained to another PR}

Author (upgrading)

• Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading}
• Added u tag to commit title _{or this PR does not require upgrading}
• Added upgrade label to PR _{or this PR does not require upgrading}

Author (operator tasks)

• Added checklist items for additional operator tasks _{or this PR does not require additional tasks}

Author (hotfixes)

• Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
• Reverted the temporary hotfix connected to the issue _{or there is no temporary hotfix for the connected issue on the prod branch}

Author (requirements)

• Ran make requirements_update _{or this PR does not touch requirements*.txt, common.mk, Makefile and Dockerfile}
• Added R tag to commit title _{or this PR does not touch requirements*.txt}
• Added reqs label to PR _{or this PR does not touch requirements*.txt}

Author (rebasing, integration test)

• make integration_test passes in personal deployment _{or this PR does not touch functionality that could break the IT}
• Rebased branch on develop, squashed old fixups

Peer reviewer (after requesting changes)

Uncheck the Author (requirements) and Author (rebasing, integration test)
checklists.

Peer reviewer (after approval)

• Ticket is in Review requested column
• Requested review from primary reviewer
• Assigned PR to primary reviewer

Primary reviewer (after requesting changes)

Uncheck the Author (requirements) and Author (rebasing, integration test)
checklists. Update the N reviews label.

Primary reviewer (after approval)

• Actually approved the PR
• Labeled connected issue as demo or no demo
• Commented on connected issue about demo expectations _{or labelled connected issue as no demo}
• Decided if PR can be labeled no sandbox
• PR title is appropriate as title of merge commit
• N reviews label is accurate
• Moved ticket to Approved column
• Assigned PR to current operator

Operator (before pushing merge the commit)

• Deployed to dev.gitlab
• Deployed to prod.gitlab
• Deployed to anvildev.gitlab
• Checked reindex label and r commit title tag
• Checked that demo expectations are clear _{or connected issue is labeled as no demo}
• Rebased and squashed branch
• Sanity-checked history
• Pushed PR branch to GitHub
• Branch pushed to GitLab and added sandbox label _{or PR is labeled no sandbox}
• Build passed in sandbox _{or PR is labeled no sandbox}
• Deleted unreferenced indices in sandbox _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Started reindex in sandbox _{or this PR does not require reindexing sandbox}
• Checked for failures in sandbox _{or this PR does not require reindexing sandbox}
• Added PR reference to merge commit title
• Collected commit title tags in merge commit title
• Moved connected issue to Merged column
• Pushed merge commit to GitHub

Operator (after pushing the merge commit)

• Shortened the PR chain _{or this PR is not labeled base}
• Pushed merge commit to GitLab _{or PR is labeled no sandbox}
• Deleted PR branch from GitHub and GitLab
• Build passes on GitLab¹

¹ When pushing the merge commit is skipped due to the PR being
labelled no sandbox, the next build triggered by a PR whose merge commit is
pushed determines this checklist item.

Operator (reindex)

• Deleted unreferenced indices in dev _{or this PR does not remove catalogs or otherwise causes unreferenced indices}
• Started reindex in dev _{or this PR does not require reindexing}
• Checked for and triaged indexing failures _{or this PR does not require reindexing}
• Emptied fail queues in target deployment _{or this PR does not require reindexing}

Operator

• Confirmed that clamscan and prune-images jobs ran on the weekend after this was deployed to dev.gitlab
• Confirmed that clamscan and prune-images jobs ran on the weekend after this was deployed to prod.gitlab
• Confirmed that clamscan and prune-images jobs ran on the weekend after this was deployed to anvildev.gitlab
• Unassigned PR

Shorthand for review comments

• L line is too long
• W line wrapping is wrong
• Q bad quotes
• F other formatting problem

[coveralls]

Coverage remained the same at 82.383% when pulling 60e384f on issues/hannes/4188-amazon-linux into fd679e3 on develop.

[codecov]

Codecov Report

Merging #4443 (60e384f) into develop (fd679e3) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #4443   +/-   ##
========================================
  Coverage    82.12%   82.12%           
========================================
  Files          131      131           
  Lines        16297    16297           
========================================
  Hits         13384    13384           
  Misses        2913     2913           

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[hannes-ucsc]

Wrong branch name.

[hannes-ucsc]

Continued in #4449